MoleditPy 2.2.0a1__py3-none-any.whl → 2.2.0a3__py3-none-any.whl

moleditpy/plugins/Optimization/conf_search.py

@@ -1,224 +0,0 @@
-from PyQt6.QtWidgets import (
-    QDialog, QVBoxLayout, QHBoxLayout, QTableWidget, 
-    QTableWidgetItem, QPushButton, QMessageBox, QLabel, QHeaderView, QAbstractItemView,
-    QApplication, QComboBox
-)
-from PyQt6.QtCore import Qt
-from rdkit import Chem
-from rdkit.Chem import AllChem
-import copy
-
-PLUGIN_NAME = "Conformational Search"
-__version__="2025.12.25"
-__author__="HiroYokoyama"
-
-class ConformerSearchDialog(QDialog):
-    def __init__(self, main_window, parent=None):
-        super().__init__(parent)
-        self.main_window = main_window
-        self.setWindowTitle("Conformational Search & Preview")
-        self.resize(400, 500)
-        
-        # メインウィンドウの分子への参照
-        self.target_mol = getattr(main_window, "current_mol", None)
-        
-        # 計算用の一時的な分子（オリジナルを汚染しないため）
-        self.temp_mol = None
-        # 生成された配座データのリスト [(Energy, ConformerID), ...]
-        self.conformer_data = []
-
-        self.init_ui()
-
-    def init_ui(self):
-        layout = QVBoxLayout(self)
-
-        # 説明ラベル
-        self.lbl_info = QLabel("Click 'Run Search' to generate conformers.\nSelect a row to preview.")
-        layout.addWidget(self.lbl_info)
-
-        # Force Field Selection
-        hbox_ff = QHBoxLayout()
-        hbox_ff.addWidget(QLabel("Force Field:"))
-        self.combo_ff = QComboBox()
-        self.combo_ff.addItems(["MMFF94", "UFF"])
-        hbox_ff.addWidget(self.combo_ff)
-        hbox_ff.addStretch()
-        layout.addLayout(hbox_ff)
-        
-        # Set default based on main window setting
-        default_method = getattr(self.main_window, "optimization_method", "MMFF_RDKIT")
-        if default_method:
-            default_method = default_method.upper()
-            if "UFF" in default_method:
-                self.combo_ff.setCurrentText("UFF")
-            else:
-                self.combo_ff.setCurrentText("MMFF94")
-
-        # 結果表示用テーブル
-        self.table = QTableWidget()
-        self.table.setColumnCount(2)
-        self.table.setHorizontalHeaderLabels(["Rank", "Energy (kcal/mol)"])
-        self.table.horizontalHeader().setSectionResizeMode(QHeaderView.ResizeMode.Stretch)
-        self.table.setSelectionBehavior(QAbstractItemView.SelectionBehavior.SelectRows)
-        self.table.setSelectionMode(QAbstractItemView.SelectionMode.SingleSelection)
-        self.table.itemClicked.connect(self.preview_conformer)
-        layout.addWidget(self.table)
-
-        # ボタンエリア
-        btn_layout = QHBoxLayout()
-        self.btn_run = QPushButton("Run Search")
-        self.btn_run.clicked.connect(self.run_search)
-        
-        self.btn_close = QPushButton("Close")
-        self.btn_close.clicked.connect(self.accept) # 閉じる（現在のプレビュー状態で確定）
-
-        btn_layout.addWidget(self.btn_run)
-        btn_layout.addWidget(self.btn_close)
-        layout.addLayout(btn_layout)
-
-    def accept(self):
-        # Push undo state when closing the dialog (confirming the selection)
-        if hasattr(self.main_window, "push_undo_state"):
-            self.main_window.push_undo_state()
-        super().accept()
-
-    def run_search(self):
-        if not self.target_mol:
-            return
-
-        self.btn_run.setEnabled(False)
-        self.lbl_info.setText("Running conformational search... please wait.")
-        QApplication.processEvents()
-
-        try:
-            # 計算用に分子を複製（水素が付加されていることを推奨）
-            mol_calc = copy.deepcopy(self.target_mol)
-            
-            # 1. 配座生成 (ETKDGv3)
-            params = AllChem.ETKDGv3()
-            params.useSmallRingTorsions = True
-            cids = AllChem.EmbedMultipleConfs(mol_calc, numConfs=30, params=params)
-
-            if not cids:
-                QMessageBox.warning(self, PLUGIN_NAME, "Failed to generate conformers.")
-                self.lbl_info.setText("Failed.")
-                self.btn_run.setEnabled(True)
-                return
-
-            # 2. 構造最適化とエネルギー計算
-            results = []
-            selected_ff = self.combo_ff.currentText()
-            
-            for i, cid in enumerate(cids):
-                energy = None
-                
-                if selected_ff == "MMFF94":
-                     # MMFF94 Optimize
-                    if AllChem.MMFFOptimizeMolecule(mol_calc, confId=cid) != -1:
-                         # Calculate Energy
-                         prop = AllChem.MMFFGetMoleculeProperties(mol_calc)
-                         if prop:
-                             ff = AllChem.MMFFGetMoleculeForceField(mol_calc, prop, confId=cid)
-                             if ff:
-                                 energy = ff.CalcEnergy()
-                
-                elif selected_ff == "UFF":
-                     # UFF Optimize
-                     if AllChem.UFFOptimizeMolecule(mol_calc, confId=cid) != -1:
-                         # Calculate Energy
-                         ff = AllChem.UFFGetMoleculeForceField(mol_calc, confId=cid)
-                         if ff:
-                             energy = ff.CalcEnergy()
-
-                if energy is not None:
-                    results.append((energy, cid))
-                
-                # UIの応答性を維持
-                if i % 5 == 0:
-                    QApplication.processEvents()
-
-            if not results:
-                 QMessageBox.warning(self, PLUGIN_NAME, f"Optimization failed with {selected_ff}.")
-                 self.btn_run.setEnabled(True)
-                 return
-
-            # エネルギーが低い順にソート
-            results.sort(key=lambda x: x[0])
-            
-            # データを保持
-            self.temp_mol = mol_calc
-            self.conformer_data = results
-
-            # テーブル更新
-            self.update_table()
-            self.lbl_info.setText(f"Found {len(results)} conformers ({selected_ff}).")
-
-        except Exception as e:
-            QMessageBox.critical(self, PLUGIN_NAME, f"Error during search: {str(e)}")
-            self.lbl_info.setText("Error occurred.")
-        finally:
-            self.btn_run.setEnabled(True)
-
-    def update_table(self):
-        self.table.setRowCount(0)
-        # base_energy = self.conformer_data[0][0] if self.conformer_data else 0
-
-        for rank, (energy, cid) in enumerate(self.conformer_data):
-            row_idx = self.table.rowCount()
-            self.table.insertRow(row_idx)
-            
-            # Rank
-            self.table.setItem(row_idx, 0, QTableWidgetItem(str(rank + 1)))
-            
-            # Energy
-            energy_str = f"{energy:.4f}"
-            self.table.setItem(row_idx, 1, QTableWidgetItem(energy_str))
-            
-            # 隠しデータとしてConformer IDを持たせる
-            self.table.item(row_idx, 0).setData(Qt.ItemDataRole.UserRole, cid)
-
-    def preview_conformer(self, item):
-        """リスト選択時にメインウィンドウの表示を更新"""
-        if not self.temp_mol or not self.target_mol:
-            return
-        
-        row = item.row()
-        # Rankカラム(0)にCIDを埋め込んでいるので取得
-        cid = self.table.item(row, 0).data(Qt.ItemDataRole.UserRole)
-        
-        # 選択された配座の座標を取得
-        source_conf = self.temp_mol.GetConformer(cid)
-        target_conf = self.target_mol.GetConformer() # 現在の表示用Conformer
-        
-        # 座標のコピー
-        for i in range(self.target_mol.GetNumAtoms()):
-            pos = source_conf.GetAtomPosition(i)
-            target_conf.SetAtomPosition(i, pos)
-            
-        # ビューの更新（ユーザー提供コードのロジックに従う）
-        if hasattr(self.main_window, "draw_molecule_3d"):
-            self.main_window.draw_molecule_3d(self.target_mol)
-        elif hasattr(self.main_window, "update_view"):
-            self.main_window.update_view()
-        elif hasattr(self.main_window, "gl_widget"):
-            # GLWidgetのリフレッシュ
-            getattr(self.main_window.gl_widget, "update", lambda: None)()
-
-def run(mw):
-    mol = getattr(mw, "current_mol", None)
-    if not mol:
-        QMessageBox.warning(mw, PLUGIN_NAME, "No molecule loaded.")
-        return
-        
-    # 既存のダイアログがあればアクティブにする
-    if hasattr(mw, "_conformer_search_dialog") and mw._conformer_search_dialog.isVisible():
-        mw._conformer_search_dialog.raise_()
-        mw._conformer_search_dialog.activateWindow()
-        return
-
-    dialog = ConformerSearchDialog(mw, parent=mw)
-    # 参照を保持してGCを防ぐ
-    mw._conformer_search_dialog = dialog
-    dialog.show() # モーダルではなくModeless（非ブロック）で表示
-
-# initialize removed as it only registered the menu action